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Old 09-14-2011, 11:33 AM   #1
Junior Member
Location: Boston

Join Date: Jul 2011
Posts: 1
Default Bowtie -n vs. -v, which one should we use?

I noticed that in Bowtie, the default is using -n, where it considering quality score. -v option does not consider quality score.

However, in Tophat, which calls Bowtie for mapping, the default is using '-v' when it calls Bowtie. I am just wondering why Tophat uses '-v' option when calling Bowtie, not '-n'?
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Old 09-14-2011, 11:38 AM   #2
Rick Westerman
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104

I do not use TopHat (at least not extensively) so can not say for sure but I suspect that it is because -n vs. -v is more than just 'use quality' vs. 'do not use quality'. Tophat probably wants the more simple and less filtered results from '-v'. See:

Last edited by westerman; 09-14-2011 at 11:43 AM. Reason: Added in 'not extensively' to clarify my Tophat usage.
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bowtie, sequencing analysis, tophat bowtie

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